We introduce a natural language interface for building stochastic \pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and transformation. This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy. We give a formal semantics for this language and a translation algorithm into stochastic \pi calculus that delivers this semantics. We demonstrate the language on a model of Fcr receptor phosphorylation during phagocytosis. We provide a tool implementation of the translation into a stochastic pi calculus language, Microsoft Research's SPiM, which can be used for simulation and analysis.
An Intuitive Modelling Interface for Systems Biology
Kahramanogullari, Ozan;
2013-01-01
Abstract
We introduce a natural language interface for building stochastic \pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and transformation. This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy. We give a formal semantics for this language and a translation algorithm into stochastic \pi calculus that delivers this semantics. We demonstrate the language on a model of Fcr receptor phosphorylation during phagocytosis. We provide a tool implementation of the translation into a stochastic pi calculus language, Microsoft Research's SPiM, which can be used for simulation and analysis.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione
